X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=7c3db2c0f080427385319e32299fab1d319f2075;hb=59d682209891099d46b960509907c79e3fb276fe;hp=abc7de76be40ebe935ab0983cdaea78c575b144b;hpb=9a0f8bd63ac90b6afad56e321a7556be3cfabd49;p=jalview.git

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index abc7de7..7c3db2c 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,4 +1,21 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+-->
 <head>
 <title>Popup Menu</title>
 </head>
@@ -11,6 +28,10 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
 <ul>
   <li><strong>Selection</strong> 
     <ul>
+      <li><a name="sqreport"><strong>Sequence Details ...<br>
+          </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
+            and database cross references</a> normally shown in the sequence's
+            tooltip.</em></li>
       <li><strong>Edit </strong> 
         <ul>
           <li><strong>Copy</strong><br>
@@ -71,13 +92,27 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
     	</em></li>
 	    	    </ul>
       </li>
+<!-- not available in 2.5 yet
+    <li><strong>Group Links<br>
+    </strong><em>This menu is only visible if there are group links available for the current selection.
+    </em> 
+    <ul>
+    <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
+    <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
+    <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
     </ul>
+    <em>Group Links were added in Jalview 2.5</em></li>
+-->    </ul>
   </li>
   <li><strong>Sequence Id<br>
     </strong><em>This menu is only visible if you right-click on a sequence name. 
     </em> 
     <ul>
-      <li><strong>Edit Name/Description<br>
+      <li><a name="sqreport"><strong>Sequence Details ...<br>
+					</strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
+						and database cross references</a> normally shown in the sequence's
+						tooltip.</em></li>
+			<li><strong>Edit Name/Description<br>
         </strong><em>You may edit the name and description of each sequence. A 
         window will be displayed asking for a new sequence name and sequence description 
         to be entered. Press OK to accept your edit. To save sequence descriptions, 
@@ -92,7 +127,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
         Connections tab.<br>
         Since Jalview 2.4, links will also be made for database cross 
         references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
-        <br>Since Jalview 2.4.1, links are also shown for non-positional sequence features attached to 
+        <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to 
         the sequence, and any regular-expression based URL links that 
         matched the description line.
         </em><strong><br>
@@ -123,10 +158,11 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
       </li>
       <li><strong>View Structure<br>
         </strong><em> If the sequence has an associated PDB file added by one 
-        of the methods described above, Jalview will display a 3D interactive 
-        viewer of the file.<br>
+        of the methods described above, Jalview will open a 3D interactive 
+        view of the file.<br>
         These entries will only be present if the sequence has <a
-			href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
+			href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
+			If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
       </li>
     </ul>
   </li>
